R: Container for coding sequence (CDS) annotation information
CDSSet
R Documentation
Container for coding sequence (CDS) annotation information
Description
A container for coding sequence annotation information.
Usage
CDSSet(cds)
Arguments
cds
A data.frame object contaning CDS annotation. See details for required columns.
Details
This object can be generated automatically from getCDS, or can be be generated manually by creating a new CDSSet from a data.frame with the following columns:
chrom, the chromosome name (NB: chromosome names must match when running annotatePTC).
strand, the strand,
cdsStart, the genomic start of the coding sequence (beware of 0/1-frame issuses), and
cdsEnd, the genomic end of the coding sequence (beware of 0/1-frame issuses).
The CDSset object is required by annotatePTC for translation of transcripts and premature termination codon annotation.
For an example, see annotatePTC.
Value
A CDSSet object.
Author(s)
Kristoffer Vitting-Seerup, Johannes Waage
References
Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.